Removing an unknown primer sequence from reads.

[mchotalia]

Hi,

Could anyone help me learn how to remove an unknown primer sequence from the ends of reads. I have these primers attached to the DNA prior to making the Illumina libraries as i have used them for other reactions. This means that when the data is compiled i have a lot of data that is unmappable due to these primers.

Any ideas?

I have to admit...i'm no bioinformatician so could you keep your replies easy for me to understand please.

Thanks in advance

[Jose Blanca]

We have develop a tool to clean different kind of sequences. It can remove adaptor sequences from solexa reads. We haven't write the documentation yet. You can take a look at the biolib project code.
To clean the sequences we use the run_cleanning_pipeline.py script.
If you're interested write me an email (jblanca _at_ btc.upv.es).

[spenthil]

Take a look at Figaro (http://sourceforge.net/apps/mediawik...p?title=Figaro).